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| Status |
Public on Dec 12, 2020 |
| Title |
NTT_2c rep1 |
| Sample type |
SRA |
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| Source name |
early embryo
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| Organism |
Bos taurus |
| Characteristics |
tissue: early embryo
developmental stage: 2-cell embryo
method: SCNT
donor cell: Vc-treated donor cell
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| Treatment protocol |
Before the reconstruction of cloned embryos, donor cells were treated with vitamin C (0.15 mM) for 3 days
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| Growth protocol |
Preimplantation embryos were cultured in G1.5/G2.5 sequential media (Vitrolife AB, Gothenburg, Sweden) in a humidified atmosphere of 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were fully washed in RNase free polyvinyl alcohol-phosphate-buffered saline (PVA- PBS). Ten embryos in each fertilized or cloned group were collected in lysis buffer containing Triton X-100 and RNase-out in water. The samples were then immediately preserved in an ultralow-temperature freezer.
Samples were first amplified according to instructions of SMARTer Ultra Low Input RNA for Illumina Kit. cDNA libraries were prepared for sequencing using standard Illumina protocols,including fragmentation, terminal repair, 3' end plus A, ligation linker, enrichment and other steps.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
NTT2c1
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| Data processing |
Illumina CASAVA v1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
Mapped to UMD3.1 whole genome using the spliced mapping algorithm of Hisat2 (version:2.0.4)
FPKM values were derived through fragments counting by Stringtie (version:1.3.0), normalization by TMM (trimmed mean of M values) and calculation by perl.
Genome_build: UMD3.1
Supplementary_files_format_and_content: gene_expression_anno.xls including FPKM values and read count for each sample.
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| Submission date |
Dec 12, 2018 |
| Last update date |
Dec 12, 2020 |
| Contact name |
Lei Zhang |
| E-mail(s) |
zlei@nwafu.edu.cn
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| Organization name |
NWAFU
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| Street address |
taicheng road
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| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL24230 |
| Series (1) |
| GSE123705 |
RNA sequencing revealed abnormal gene expression and benefits of vitamin C treatment in cloned bovine embryos |
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| Relations |
| BioSample |
SAMN10585524 |
| SRA |
SRX5126583 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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